/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview is free software: you can redistribute it and/or
 * modify it under the terms of the GNU General Public License 
 * as published by the Free Software Foundation, either version 3
 * of the License, or (at your option) any later version.
 *  
 * Jalview is distributed in the hope that it will be useful, but 
 * WITHOUT ANY WARRANTY; without even the implied warranty 
 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 * PURPOSE.  See the GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.datamodel;

/**
 * A bean that models a point with (x, y, z) coordinates and a reference to a
 * sequence
 */
public class SequencePoint
{
  /*
   * Associated alignment sequence, or dummy sequence object
   */
  private final SequenceI sequence;

  /*
   * x, y, z position in 3-D space
   */
  public Point coord;

  /**
   * Constructor
   * 
   * @param sequence
   * @param coord
   */
  public SequencePoint(SequenceI sequence, Point pt)
  {
    this.sequence = sequence;
    this.coord = pt;
  }

  /**
   * Constructor given a sequence and an array of x, y, z coordinate positions
   * 
   * @param sequence
   * @param coords
   * @throws ArrayIndexOutOfBoundsException
   *           if array length is less than 3
   */
  public SequencePoint(SequenceI sequence, float[] coords)
  {
    this(sequence, new Point(coords[0], coords[1], coords[2]));
  }

  public SequenceI getSequence()
  {
    return sequence;
  }

  /**
   * Applies a negative translation of the 'shift' (x, y, z) coordinates
   * 
   * @param centre
   */
  public void translateBack(Point shift)
  {
    float x = coord.x - shift.x;
    float y = coord.y - shift.y;
    float z = coord.z - shift.z;

    coord = new Point(x, y, z);
  }

  /**
   * Applies a positive translation of the 'shift' (x, y, z) coordinates
   * 
   * @param centre
   */
  public void translate(Point shift)
  {
    float x = coord.x + shift.x;
    float y = coord.y + shift.y;
    float z = coord.z + shift.z;

    coord = new Point(x, y, z);
  }
}